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- EMDB-41404: Local cryo-EM refinement map (Chain C N-terminal domain) for magn... -

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Basic information

Entry
Database: EMDB / ID: EMD-41404
TitleLocal cryo-EM refinement map (Chain C N-terminal domain) for magnesium depleted CorA in complex with conformation-specific synthetic antibody C18, State MGD-1D
Map dataLocal refinement map using mask around CorA Chain C N-terminal domain, residues 1-260.
Sample
  • Complex: Magnesium-free CorA in complex with conformation-specific sAB C18
KeywordsIon Channel / Magnesium Channel / MEMBRANE PROTEIN
Biological speciesThermotoga maritima (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsErramilli SK / Perozo E / Kossiakoff AA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117372 United States
CitationJournal: To Be Published
Title: Structural basis for CorA channel gating using conformation-specific synthetic antibodies
Authors: Erramilli SK / Nosol K / Pietrzak-Lichwa K / Li T / Dutka P / Hou J / Zhao M / Perozo E / Kossiakoff AA
History
DepositionAug 1, 2023-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41404.png

Downloads & links

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Map

FileDownload / File: emd_41404.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refinement map using mask around CorA Chain C N-terminal domain, residues 1-260.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 382.68 Å		1.06 Å/pix.
x 360 pix.
= 382.68 Å		1.06 Å/pix.
x 360 pix.
= 382.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.063 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.46405798 - 0.9425399
Average (Standard dev.)0.000432685 (±0.011496198)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 382.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41404_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41404_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41404_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Magnesium-free CorA in complex with conformation-specific sAB C18

EntireName: Magnesium-free CorA in complex with conformation-specific sAB C18
Components
  • Complex: Magnesium-free CorA in complex with conformation-specific sAB C18

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Supramolecule #1: Magnesium-free CorA in complex with conformation-specific sAB C18

SupramoleculeName: Magnesium-free CorA in complex with conformation-specific sAB C18
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Thermotoga maritima (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 12478 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 44836
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: Coot

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